--- a
+++ b/man/Cohesion.Rd
@@ -0,0 +1,56 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/7.stability.R
+\name{Cohesion}
+\alias{Cohesion}
+\alias{plot.cohesion}
+\title{Cohesion calculation}
+\usage{
+Cohesion(otutab, reps = 200, threads = 1, mycor = NULL, verbose = TRUE)
+
+\method{plot}{cohesion}(x, group, metadata, mode = 1, ...)
+}
+\arguments{
+\item{otutab}{otutab}
+
+\item{reps}{iteration time}
+
+\item{threads}{threads}
+
+\item{mycor}{a correlation matrix you want to use, skip the null model build when mycor is not NULL, default: NULL}
+
+\item{verbose}{verbose}
+
+\item{x}{\code{Cohesion()} result (cohesion object)}
+
+\item{group}{group name in colnames(metadata)}
+
+\item{metadata}{metadata}
+
+\item{mode}{plot mode, 1~2}
+
+\item{...}{additional arguments for \code{\link[pcutils]{group_box}} (mode=1) or \code{\link[pcutils]{group_box}} (mode=2)}
+}
+\value{
+Cohesion object: a list with two dataframe
+
+a ggplot
+}
+\description{
+Cohesion calculation
+
+Plot cohesion
+}
+\examples{
+\donttest{
+data("otutab", package = "pcutils")
+# set reps at least 99 when you run.
+Cohesion(otutab[1:50, ], reps = 19) -> cohesion_res
+if (requireNamespace("ggpubr")) {
+  plot(cohesion_res, group = "Group", metadata = metadata, mode = 1)
+  plot(cohesion_res, group = "Group", metadata = metadata, mode = 2)
+}
+}
+}
+\references{
+Herren, C. M. & McMahon, K. (2017) Cohesion: a method for quantifying the connectivity of microbial communities. doi:10.1038/ismej.2017.91.
+}